The answer to this question can be found in the Epilogue of the book. Specifically, it can be found on page 17 of the paperback edition of the book.
On p. 17, Diamond has just set out “Yali’s question.” This question asks why Europeans had so much “cargo” while people from New Guinea did not. In other words, Yali was asking why some groups are dominant and others are not. Diamond then notes that some people think that it is a bad idea to try to answer a question like the one that Yali raises. He says that some people have the following concern:
If we succeed in explaining how some people came to dominate other people, may this not seem to justify the domination?
What Diamond is saying is that some people think that explaining a certain condition is the same thing as saying that it is right for the condition to exist. If we explain why the Europeans came to dominate the world, we will be saying that it is right for Europeans to do so.
Thus, the worry is that we will be justifying the domination of some groups by others and making it more likely that this domination will continue.